Botulinum neurotoxins (BoNTs) are the deadliest of microbial toxins. The enzymes' Zinc(II) metalloprotease, referred to as the light chain (LC) component, inhibits acetylcholine release into neuromuscular junctions, resulting in the disease botulism. Currently, no therapies counter BoNT poisoning post-neuronal intoxication; however, it is hypothesized that small molecules may be used to inhibit BoNT LC activity in the neuronal cytosol. Herein, we describe the pharmacophore-based design and chemical synthesis of potent (non-Zinc(II) chelating) small molecule (non-peptidic) inhibitors (SMNPIs) of the BoNT serotype A LC (the most toxic of the BoNT serotype LCs). Specifically, the three-dimensional superimpositions of 2-[4-(4-amidinephenoxy)-phenyl]-indole-6-amidine-based SMNPI regioisomers (K(i) = 0.600 μM (± 0.100 μM)), with a novel lead bis-[3-amide-5-(imidazolino)-phenyl]-terephthalamide (BAIPT)-based SMNPI (K(i) = 8.52 μM (± 0.53 μM)), resulted in a refined 4-zone pharmacophore. The refined model guided the design of BAIPT-based SMNPIs possessing K(i) values = 0.572 μM (± 0.041 μM) and 0.900 μM (± 0.078 μM).